1XME
Structure of Recombinant Cytochrome ba3 Oxidase from Thermus thermophilus
- PDB DOI: https://doi.org/10.2210/pdb1XME/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Thermus thermophilus
- Expression System: Thermus thermophilus HB8
- Mutation(s): No 
- Membrane Protein: Yes  PDBTMMemProtMD
- Deposited: 2004-10-01 Released: 2005-03-22 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.236 
- R-Value Work: 0.217 
- R-Value Observed: 0.217 
This is version 1.4 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Cytochrome c oxidase polypeptide I | 568 | Thermus thermophilus | Mutation(s): 0  Gene Names: cbaA EC: 1.9.3.1 Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for Q5SJ79 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ79  Go to UniProtKB:  Q5SJ79 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q5SJ79 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Cytochrome c oxidase polypeptide II | 168 | Thermus thermophilus | Mutation(s): 0  Gene Names: cbaB, ctaC EC: 1.9.3.1 Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for Q5SJ80 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ80  Go to UniProtKB:  Q5SJ80 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q5SJ80 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Cytochrome c oxidase polypeptide IIA | 34 | Thermus thermophilus | Mutation(s): 0  Gene Names: cbaD EC: 1.9.3.1 Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for P82543 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P82543  Go to UniProtKB:  P82543 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P82543 | ||||
Sequence AnnotationsExpand | |||||
|
Small Molecules
Ligands 6 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
HAS Query on HAS | G [auth A] | HEME-AS C54 H64 Fe N4 O6 PDYODZVCODUKFH-ZOMLSHGTSA-L | |||
HEM Query on HEM | F [auth A] | PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L | |||
BNG Query on BNG | D [auth A] | nonyl beta-D-glucopyranoside C15 H30 O6 QFAPUKLCALRPLH-UXXRCYHCSA-N | |||
CUA Query on CUA | I [auth B] | DINUCLEAR COPPER ION Cu2 ALKZAGKDWUSJED-UHFFFAOYSA-N | |||
GOL Query on GOL | H [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
CU Query on CU | E [auth A] | COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.236 
- R-Value Work: 0.217 
- R-Value Observed: 0.217 
- Space Group: P 43 21 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 114.902 | α = 90 |
b = 114.902 | β = 90 |
c = 177.064 | γ = 90 |
Software Name | Purpose |
---|---|
CNS | refinement |
MOSFLM | data reduction |
CCP4 | data scaling |
MOLREP | phasing |
Entry History 
Deposition Data
- Released Date: 2005-03-22  Deposition Author(s): Hunsicker-Wang, L.M., Pacoma, R.L., Chen, Y., Fee, J.A., Stout, C.D.
Revision History (Full details and data files)
- Version 1.0: 2005-03-22
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary - Version 1.4: 2023-08-23
Changes: Data collection, Database references, Refinement description, Structure summary